Get things underway early. It’s estimated that at least 20 million of the 130 million population of Japan reside in Tokyo, Osaka, and Kyoto — that’s as many as Los Angeles and New York combined. The frequent-flyer-approach to travel will hit you by surprise. The standard trip to Japan will yield highs and lows; the all-inclusive commuter trips to Tokyo will feel interminable (at least in the air), and can leave you with the feel that you don’t really have enough to do. But skipping straight through to pre-priced sightseeing hubs and following longer routes to the gateway cities will lead to better travel experiences, as tourists discover lesser-known locals and idyllic locations that will get you feeling at home. It won’t be a glossy storybook experience — real, non-guidebook items often scratch a nerve — but you’ll learn more than you can get from Lonely Planet. Remember, there’s a city of trains in Japan, not only a city of cities.
Filing the paperwork can be an arduous endeavor. Tokyo is international. Some countries require the passport to be renewed frequently, often every three to five years. Some countries (including Australia and the U.S.) enforce a specific “simplified renewal” form (1,2,3) that can’t be downloaded online, only signed. Japan is unique — anyone who wants a Japanese passport can receive one (and upgrade it to a DS) and there’s no passport agency to run to.